Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard
Repeated Whole-Genome Duplication, Karyotype Reshuffling, and Biased Retention of Stress-Responding Genes in Buckler Mustard
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DOI：
10.1105/tpc.15.00791
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发表时间：
2016-01-01
期刊：
影响因子：
11.6
通讯作者：
Parisod, Christian
中科院分区：
文献类型：
--
作者：
Geiser, Celine;Mandakova, Terezie;Parisod, Christian
全基因组复制（WGD）通常伴随着基因丢失和核型重新模式。尽管有证据表明新的适应性特征与 WGD 相关，但这种基因组分离的基础和进化意义仍然难以捉摸。在这里，我们使用 Buckler Mustard (Biscutella laevigata) 来推断在反复 WGD 后驱动重复基因保留的过程。除了所有十字花科共有的 β- 和 α-WGD 事件外，细胞遗传学和转录组分析还揭示了圆叶芥 (Biscutelleae) 分支在环境变化时发生的两个较年轻的 WGD 事件：中新世晚期的中多倍体事件，随后发生了相当大的核型重组和染色体数量减少，以及更新世期间的新多倍体事件。尽管相当数量的较老的重复在正选择下呈现出保留的特征，但由较年轻的中多倍体WGD事件产生的大多数保留的重复与基因平衡假说的预测相匹配，并显示出强烈的纯化选择以及响应非生物应激源的基因类别富集的证据。两个基因组拷贝中大段染色体的保留支持了这样的假设，即全基因组测序和偏向分馏的循环塑造了这种耐应激多倍体的基因组，促进了面对环境挑战时应激反应基因的适应性募集。
Whole-genome duplication (WGD) is usually followed by gene loss and karyotype repatterning. Despite evidence of new adaptive traits associated with WGD, the underpinnings and evolutionary significance of such genome fractionation remain elusive. Here, we use Buckler mustard (Biscutella laevigata) to infer processes that have driven the retention of duplicated genes after recurrent WGDs. In addition to the beta- and alpha-WGD events shared by all Brassicaceae, cytogenetic and transcriptome analyses revealed two younger WGD events that occurred at times of environmental changes in the clade of Buckler mustard (Biscutelleae): a mesopolyploidy event from the late Miocene that was followed by considerable karyotype reshuffling and chromosome number reduction and a neopolyploidy event during the Pleistocene. Although a considerable number of the older duplicates presented signatures of retention under positive selection, the majority of retained duplicates arising from the younger mesopolyploidy WGD event matched predictions of the gene balance hypothesis and showed evidence of strong purifying selection as well as enrichment in gene categories responding to abiotic stressors. Retention of large stretches of chromosomes for both genomic copies supported the hypothesis that cycles of WGD and biased fractionation shaped the genome of this stress-tolerant polypolyloid, promoting the adaptive recruitment of stress-responding genes in the face of environmental challenges.